Macoto Kikuchi

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Name
Macoto Kikuchi
E-mail
kikuchicmc.osaka-u.ac.jp
Research funding number
50195210

Academic & Professional Experience

 
2000
 - 
Today
Professor, Cybermedia Center, Osaka University
 

Published Papers

 
A.Nakayama, M.Kikuchi, A.Shibata, Y.Sugiyama, S.Tadaki and S.Yukawa
Traffic and Granular Flow '15   523-530   Sep 2016   [Refereed]
Shin-ichi Tadaki, Macoto Kikuchi, Akihiro Nakayama, Akihiro Shibata, Yuki Sugiyama and Satoshi Yukawa
New J. Phys.   18 83022   Aug 2016   [Refereed]
From a physics point of view, the emergence of a traffic jam is considered to be a dynamical phase transition. To verify this, we performed a series of circuit experiments. In previous work, Tadaki et al (2013 New J. Phys 15 103034), we confirmed ...
Akihiro Nakayama, Macoto Kikuchi, Akihiro Shibata, Yuki Sugiyama, Shin-ichi Tadaki, Satoshi Yukawa
New J. Phys.   18 43040   Apr 2016   [Refereed]
Nobu C. Shirai and Macoto Kikuchi
J. Chem. Phys.   144 55101   Feb 2016   [Refereed]
?-synuclein (?-syn) is an intrinsically disordered protein which is considered to be one of the causes of Parkinson’s disease. This protein forms amyloid fibrils when in a highly concentrated solution. The fibril formation of ?-syn is induced not ...
Ryo Kanada, Fumiko Takagi, Macoto Kikuchi
Proteins: Structure, Function, and Bioinformatics   83(5) 809-819   May 2015   [Refereed]
Molecular motors such as kinesin regulate affinity to a rail protein during the ATP hydrolysis cycle. The regulation mechanism, however, is yet to be determined. To understand this mechanism, we investigated the structural fluctuations of the moto...
Akimasa Kitajima, Macoto Kikuchi
PLOS ONE   10 e0125062   May 2015   [Refereed]
How rare are magic squares? So far, the exact number of magic squares of order n is only known for n 5. For larger squares, we need statistical approaches for estimating the num- ber. For this purpose, we formulated the problem as a combinatorial ...
Nobu C. Shirai, Macoto Kikuchi
J. Chem. Phys.   139 225103   Dec 2013   [Refereed]
An intrinsically disordered protein (IDP) lacks a stable three-dimensional structure, while it folds into a specific structure when it binds to a target molecule. In some IDP-target complexes, not all target binding surfaces are exposed on the out...
Shin-ichi Tadaki, Macoto Kikuchi, Minoru Fukui, Akihiro Nakayama, Katsuhiro Nishinari, Akihiro Shibata, Yuki Sugiyama, Taturu Yosida and Satoshi Yukawa
New J. Phys.   15 103034   Oct 2013   [Refereed]
The emergence of a traffic jam is considered to be a dynamical phase transition in a physics point of view; traffic flow becomes unstable and changes phase into a traffic jam when the car density exceeds a critical value. In order to verify this v...
Katsuyoshi Matsushita and Macoto Kikuchi
J, Phys,: Conference Series   454 12034   Aug 2013   [Refereed]
Nobu C Shirai and Macoto Kikuchi
J, Phys,: Conference Series   454 12039   Aug 2013   [Refereed][Invited]
Nen Saito and Macoto Kikuchi
New J. Phys.   15 53037   May 2013   [Refereed]
Dynamics in biological networks are, in general, robust against several perturbations. We investigate a coupled map network as a model motivated by gene regulatory networks and design systems that are robust against phenotypic perturbations (pertu...
Katsuyoshi Matsushita and Macoto Kikuchi
J. Chem. Phys.   138(10) 105101   Mar 2013   [Refereed]
Atsunari Katsuki and Macoto Kikuchi
New J. Phys.   13 3049   Jun 2011   [Refereed]
A group of barchans, crescent sand dunes, exhibit a characteristic flying-geese pattern in deserts on Earth and Mars. This pattern implies that an indirect interaction between barchans, mediated by an inter-dune sand stream, which is released from...
Katsuki, A., Kikuchi, M., Nishimori, H., Endo, N. and Taniguchi, K.
Earth Surface Processes and Landforms   36 372-382   Mar 2011   [Refereed]
Barchans are crescent-shaped dunes that form under unidirectional wind in areas of limited sand supply. The recent development of flume experiments and computer simulations has renewed interest in the interaction dynamics of two or more barchans. ...
Eureka in the Age of Science and Pseudoscience
Macoto Kikuchi
Journal of the Poe Society of Japan   1 61   Sep 2009   [Invited]
Akihiro Nakayama, Minoru Fukui, Macoto Kikuchi, Katsuya Hasebe, Katsuhiro Nishinari, Yuki Sugiyama, Shin-ichi Tadaki and Satoshi Yukawa
New J. Phys.   11 83025   Aug 2009   [Refereed]
Renormalization Group and Condensed Matter Physics: Critical Phenomena and Beyond
Macoto Kikuchi and Yutaka Okabe
数理科学   (553)    Jul 2009   [Invited]
Hiroo Kenzaki and Macoto Kikuchi
Proteins: Structure, Function, and Bioinformatics   71(1) 389-395   Apr 2008   [Refereed]
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with G? interactions. By means of the multi-self-overlap ensemble Monte Carlo method and the principal component analysis, the...
Yuki Sugiyama, Minoru Fukui, Macoto Kikuchi, Katsuya Hasebe, Akihiro Nakayama, Katsuhiro Nishinari, Shin-ichi Tadaki and Satoshi Yukawa
New J. Phys.   10 33001   Mar 2008   [Refereed]
A traffic jam on a highway is a very familiar phenomenon. From the physical viewpoint, the system of vehicular flow is a non-equilibrium system of interacting particles (vehicles). The collective effect of the many-particle system induces the inst...
Hiromitsu Shimoyama and Macoto Kikuchi
J. Phys. Soc. Jpn.   76(10) 103801   Oct 2007   [Refereed]
It is widely accepted that the folding process of a protein is in large part determined by topology of the native structure. A class of coarse-grained model called Go-like model that takes only the native-state topology into account has successful...
Fumiko Takagi and Macoto Kikuchi
Biophys, J.   93 3820-3827   Aug 2007   [Refereed]
We investigated the structural relaxation of myosin motor domain from the pre-power stroke state to the near-rigor state using molecular dynamics simulation of a coarse-grained protein model. To describe the spontaneous structural change, we propo...
Hiroo Kenzaki and Macoto Kikuchi
Chem. Phys. Lett.   427(4-6) 414-417   Aug 2006   [Refereed]
To elucidate the role of relative stability of subdomains in folding processes of multi-domain proteins, we have studied a free-energy landscape of c-type lysozyme by Monte Carlo simulations using a realistic lattice model with a G?-like interacti...
Kazuki Nakanishi and Macoto Kikuchi
J. Phys. Soc. Jpn.   75(6) 64803   May 2006   [Refereed]
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-self-overlap-ensemble Monte Carlo method is used for n...
Hiroo Kenzaki and Macoto Kikuchi
Chem. Phys. Lett.   422(4-6) 429-433   May 2006   [Refereed]
S. Tadaki, M. Kikuchi, A. Nakayama, K. Nishinari, A. Shibata, Y. Sugiyama and S. Yukawa
J. Phys. Soc. Jpn.   75 34002   Mar 2006   [Refereed]
A. Katsuki, M. Kikuchi, and N. Endo
J. Phys. Soc. Jpn.   74 878-881   Mar 2005   [Refereed]
We observed the time evolution of dune fields in a water tank experiment and simulated it by using a simple model without taking complex fluid dynamics into account. The initial sand bed changed its form to transverse ripples, that is, dunes with ...
Long-Term Traffic Data from Japanese Expressway
M. Kikuchi, A. Nakayama, K. Nishinari, Y. Sugiyama, S. Tadaki and S. Yukawa
Traffic and Granular Flow '01      Apr 2003   [Refereed]
Observational Aspects of Japanese Highway Traffic
S. Yukawa, M. Kikuchi, A. Nakayama, K. Nishinari, Y. Sugiyama and S. Tadaki
Traffic and Granular Flow '01      Apr 2003   [Refereed]
Congestion Induced by Bottlenecks in Two-lane Optimal Velocity Traffic Flow Model
S. Tadaki, M. Kikuchi, K. Nishinari, Y. Sugiyama and S. Yukawa
Traffic and Granular Flow '01      Apr 2003   [Refereed]
Macoto Kikuchi
応用数理   12(2) 104   Jun 2002   [Invited]
As an introduction to the special topics section of traffic flow problem, a brief history of mathematical researches in this area is described. Some basic concepts, such as a q-k diagram, are introduced at the same time.

「特集:高速道路交通の数理」序論
S. Tadaki, K. Nishinari, M. Kikuchi, Y. Sugiyama and S. Yukawa
Physica A   315 156-162   Apr 2002   [Refereed]
S. Tadaki, K. Nishinari, M. Kikuchi, Y. Sugiyama and S. Yukawa
J. Phys. Soc. Jpn.,   71(9) 2326-2334   Apr 2002   [Refereed]
Congestion in Multi-lane Coupled Map Traffic FLow Model
Shin-ichi Tadaki, Macoto Kikuchi, Yuki Sugiyama and Satoshi Yukawa
AIP Conference Proceedings   519(1) 578   Apr 2001   [Refereed]
Dynamical Equation Approach to Protein Design
Kei Tokita, Macoto Kikuchi and Yukito Iba
Prog. Theor. Phys. Supple.      Jun 2000   [Refereed]
Congestion in Multi-Lane Roads with Coupled Map Traffic Flow Model
Shin-ichi Tadaki, Macoto Kikuchi, Yuki Sugiyama, and Satoshi Yukawa
Prog. Theor. Phys. suppl. 138 (2000) 594-595      Apr 2000   [Refereed]
Asymmetric Optimal Velocity Model for Traffic Flow
Macoto Kikuchi, Yuki Sugiyama, Shin-ichi Tadaki, and Satoshi Yukawa
Prog. Theor. Phys. suppl. 138 (2000) 549-554      Apr 2000   [Refereed]
Effects of Shape and Boundary Conditions on Finite-Size Scaling Functions for Anisotropic Three-Dimensional Ising Systems
Kazuhisa Kaneda, Yutaka Okabe, and Macoto Kikuchi
Prog. Theor. Phys. suppl. 138 (2000) 458-459      Apr 2000   [Refereed]
The Relation among Thermodynamic Stability, Folding Dynamics, and Designability
Rie Tatsumi, George Chikenji, Yasuhiro Akutsu, and Macoto Kikuchi
Prog. Theor. Phys. suppl. 138 (2000) 420-421      Apr 2000   [Refereed]
A Lattice Model Study of alpha-beta Transitions in Protein Folding
George Chikenji and Macoto Kikuchi
Prog. Theor. Phys. suppl. 138 (2000) 406-407      Apr 2000   [Refereed]
Multi-Selfoverlap-Ensemble Monte Carlo Method for Lattice Proteins and Heteropolymers
Macoto Kikuchi, George Chikenji, and Yukito Iba
Prog. Theor. Phys. suppl. 138 (2000) 404-405.      Apr 2000   [Refereed]
George Chikenji and Macoto Kikuchi
Proc. Natl. Acad. Sci. 97 (2000) 14273-14277.      Apr 2000   [Refereed]
The mechanism of α→β transition in folding of β-lactoglobulin is discussed based on free energy landscape analysis of a long lattice model. It is found that helical propensity of β-lactoglobulin is driven by conformational entropy and is intrinsic...
K. Kaneda, Y. Okabe, and M. Kikuchi
J. Phys. A: Math. Gen. 32 (No. 42) (1999) 7263-7271.      Apr 1999   [Refereed]
S. Tadaki, M. Kikuchi, Y. Sugiyama and S. Yukawa
J. Phys. Soc. Jpn.   68(9) 3110-3114   Apr 1999   [Refereed]
G. Chikenji, M. Kikuchi, and Y. Iba
Phys. Rev. Lett.   83(9) 1886-1889   Apr 1999   [Refereed]
Long chains of the HP lattice protein model are studied by the multi-self-overlap ensemble Monte Carlo method, which was developed recently by Iba, Chikenji, and Kikuchi. This method successfully finds the lowest energy states reported before for ...
Y. Okabe, K. Kaneda, M. Kikuchi, and C.K. Hu
Phys. Rev. E   59 1585-1588   Apr 1999   [Refereed]
Yukito Iba, Kei Tokita and Macoto Kikuchi
Journal of Physical Society of Japan   67(11) 3985-3990   Nov 1998   [Refereed]
A novel approach to heteropolymer design is proposed. It is based on the criterion by Kurosky and Deutsch, with which the probability of a target conformation in a conformation space is maximized at low but finite temperature. The key feature of t...
Y. Iba, G. Chikenji, and M. Kikuchi
J. Phys. Soc. Jpn.   67(10) 3327-3330   Apr 1998   [Refereed]
A novel family of dynamical Monte Carlo algorithms for lattice polymers is proposed. Our central idea is to simulate an extended ensemble in which the self-avoiding condition is systematically weakened. The degree of self-overlap is controlled in ...
S. Tadaki, M. Kikuchi, Y. Sugiyama and S. Yukawa
J. Phys. Soc. Jpn.   67(7) 2270-2276   Apr 1998   [Refereed]
A coupled map traffic flow model is introduced, based on optimal velocity functions. The model is simulated under open boundary conditions. Effects of noises in velocity are investigated. The average car density increases with the noise level. The...
Coupled-Map Modeling of One-Dimensional Traffic Flow
S. Yukawa and M. Kikuchi
Traffic and Granular Flow '97      Apr 1998   [Refereed]
G. Tatara, M. Kikuchi, S. Yukawa and H. Matsukawa
J. Phys. Soc. Jpn.   67(4) 1090-1093   Apr 1998   [Refereed]
Quantum mechanical motion of a particle in a periodic asymmetric potential is studied theoretically at zero temperature. It is shown based on a semi-classical approximation that the tunneling probability from one local minimum to the next becomes ...
S. Yukawa, M. Kikuchi, G. Tatara and H. Matsukawa
J. Phys. Soc. Jpn.   66(10) 2953-2956   Apr 1997   [Refereed]
Statistical Dependence Analysis
M. Kikuchi, N. Ito and Y. Okabe
Int. J. Mod. Phys. C   7 379-387   Apr 1996   [Refereed]
Universal Finite-Size-Scaling Functions
Y. Okabe and M. Kikuchi
Int. J. Mod. Phys. C   7 287-294   Apr 1996   [Refereed]
T. Nishino, K. Okunishi, and M. Kikuchi
Phys. Lett. A   213 69-72   Apr 1996   [Refereed]
We apply a recently developed numerical renormalization group, the corner-transfer-matrix renormalization group (CTMRG), to 2D classical lattice models at their critical temperatures. It is shown that the combination of CTMRG and the finite-size s...
S. Yukawa and M. Kikuchi
J. Phys. Soc. Jpn.   65(4) 916-919   Apr 1996   [Refereed]
M. Kikuchi and Y. Okabe
International J. Mod. Phys. C   6 747-763   Apr 1995   [Refereed]
The multi-spin coding of the Monte Carlo simulation of the three-state Potts model on the simple cubic lattice is presented. The ferromagnetic (F) model, the antiferromagnetic (AF) model, and the random mixture of the F and AF couplings are treate...
S. Tadaki and M. Kikuchi
J. Phys. Soc. Jpn.   64(12) 4504-4508   Apr 1995   [Refereed]
Phase Transition of the Random Potts Model
Y. Okabe and M. Kikuchi
Computational Physics as a New Frontier in Condensed Matter Research      Apr 1995   [Refereed]
S. Yukawa, M. Kikuchi
J. Phys. Soc. Jpn.   64(1) 35-38   Apr 1995   [Refereed]
We propose a new model of one-dimensional traffic flow using a coupled map lattice. In the model, each vehicle is assigned a map and changes its velocity according to it. A single map is designed so as to represent the motion of a vehicle properly...
Monte Carlo Studies of Phase Transitions in Polymer Blends and Block Copolymer Melts
K. Binder, H.-P. Deutsch, M. Mueller, H. Fried and M. Kikuchi
Il Nuovo Cimento   16D 653-660   Apr 1994   [Refereed]
S. Yukawa, M. Kikuchi, and S. Tadaki
J. Phys. Soc. Jpn.   63(10) 3609-3618   Apr 1994   [Refereed]
Effects of a bottleneck in a linear trafficway is investigated using a simple cellular automaton model. Introducing a blockage site which transmit cars at some transmission probability into the rule-184 cellular automaton, we observe three differe...
Statistical Dependence and Related Topics
M. Kikuchi, N. Ito, and Y. Okabe
Computer Simulations in Condensed Matter Physics VII      Apr 1994   [Refereed]
S. Tadaki and M. Kikuchi
Phys. Rev. E   50 4564-4570   Apr 1994   [Refereed]
M. Kikuchi and K. Binder
J. Chem. Phys.   101 3367-3377   Apr 1994   [Refereed]
By means of Monte Carlo simulations of a lattice model, microphase separation transition of symmetric diblock‐copolymer melts confined in the thin‐film geometry between parallel hard walls is studied. We impose a surface field which acts repulsive...
M. Kikuchi and N. Ito
J. Phys. Soc. Jpn.   62(9) 3052-3061   Apr 1993   [Refereed]
A new method for studying dynamical correlation of temporal sequence is proposed. We introduce a new quantity named statistical dependence time τ dep as an estimator for the equilibrium relaxation time. The calculation of τ dep does not require ca...
Recycle of Random Sequences
N. Ito, M. Kikuchi and Y. Okabe
International J. of Mod. Phys. C   4 569-590   Apr 1993   [Refereed]
M. Kikuchi and K. Binder
Europhys. Lett.   21 427-432   Apr 1993   [Refereed]
H. Kawamura and M. Kikuchi
Phys. Rev. B   47 1134-1137   Apr 1993   [Refereed]
A numerical method to study defect-mediated phase transitions is proposed, which combines a standard Monte Carlo technique with a particular type of boundary conditions. The method is applied to the two-dimensional XY (plane rotator) model as well...
Random three-state Potts model: a Monte Carlo study
Y. Okabe and M. Kikuchi
Computer Aided Innovation of New Materials II      Apr 1993   [Refereed]
Application of Finite-Size Scaling to Phase Transitions and Localization-Delocalization Transitions
Y. Okabe, M. Kikuchi and K. Niizeki
Computer Simulations in Condensed Matter Physics V,,1992,D.~P. Landau      Apr 1992   [Refereed]
M. Kikuchi and Y. Okabe
J. Phys. Soc. Jpn.   61(10) 3503-3510   Apr 1992   [Refereed]
Monte Carlo Study of Random Potts Model
Y. Okabe and M. Kikuchi
Computational Approaches in Condensed-Matter Physics      Apr 1992   [Refereed]
Free-Vortex Formation of the Plane Rotator Model
M. Kikuchi and H. Kawamura
J. Mag. Mag. Mat. ( proc. ICM91 ).   104-107 227-228   Apr 1992   [Refereed]
Monte Carlo Renormalization Group Study of Random Three-State Potts Model
M. Kikuchi and Y. Okabe
J. Mag. Mag. Mat. ( proc. ICM91 ).   104-107 209-210   Apr 1992   [Refereed]
Block-Spin Distribution Functions at Criticality
M. Kikuchi
Prog. Theor. Phys. supple.   101 557-566   Apr 1990   [Refereed]
M. Kikuchi, Y. Okabe, and S. Miyashita
J. Phys. Soc. Jpn.   59(2) 492-496   Apr 1990   [Refereed]
We study the effect of anisotropy for the ground state of the spin 1/2 antiferromagnet on the square lattice by diagonalizing the Hamiltonian numerically. The symmetry change of the ground state at the isotropic point is discussed.
Numerical Studies of Two-Dimensional Quantum Spin Systems
Y. Okabe and M. Kikuchi
Quantum Simulations of Condensed Matter Phenomena      Apr 1990   [Refereed]
M. Kikuchi and Y. Okabe
J. Phys. Soc. Jpn.   58 679-683   Apr 1989   [Refereed]
T. Nishino, M. Kikuchi, and J. Kanamori
Solid State Commun.   68 455-458   Apr 1988   [Refereed]
Y. Okabe, M. Kikuchi, and A.~D.~S. Nagi
Phys. Rev. Lett.   61 2971-2971   Apr 1988   [Refereed]
Monte Carlo Study of Quantum Spin Systems on the Square Lattice
Y. Okabe and M. Kikuchi
J. Phys. (Paris) suppl. (proc. ICM88)   C8 1393-1394   Apr 1988   [Refereed]
Y. Okabe and M. Kikuchi
J. Phys. Soc. Jpn.   57(12) 4351-4358   Apr 1988   [Refereed]
We systematically study the spin 1/2 quantum XXZ model on the square lattice using a quantum Monte Carlo method. The temperature dependence of the energy, specific heat and order parameter is calculated for the systems of sizes up to 16×16. Invest...
Growth Process of Order Parameter -- Block Spin Analysis --
M. Kikuchi and Y. Okabe
Dynamics of Ordering Processes in Condensed Matter      Apr 1987   [Refereed]
M. Kikuchi and Y. Okabe
Prog. Theor. Phys.   78(3) 540-551   Apr 1987   [Refereed]
We propose a simple method of Monte Carlo renormalization group. Thermodynamic quantities of the block-spin system are analyzed phenomenologically on the basis of scaling concept. The field exponent yH is obtained from the square of block-spin mag...
Y. Okabe and M. Kikuchi
J. Phys. Soc. Jpn.   56(6) 1963-1973   Apr 1987   [Refereed]
M. Kikuchi and Y. Okabe
Phys. Rev. B   35 5382-5384   Apr 1987   [Refereed]
We present a new method for studying the temporal evolution of order-parameter structure. The relaxation of the block-spin magnetization ratio of the three-dimensional kinetic Ising model is investigated by use of a Monte Carlo simulation with a b...
High-Speed Algorithm for Quantum Monte Carlo Simulation
Y. Okabe and M. Kikuchi
Quantum Monte Carlo Methods in Equilibrium and Nonequilibrium Systems      Apr 1987   [Refereed]
Y. Okabe and M. Kikuchi
Phys. Rev. B   34 7896-7900   Apr 1986   [Refereed]
M. Kikuchi and Y. Okabe
J. Phys. Soc. Jpn.   55 1359-1363   Apr 1986   [Refereed]
We report a Monte Carlo study on the critical relaxation of the three-dimensional kinetic Ising model from a nonequilibrium initial state. It is shown that the details of the method, namely, a choice of the sampling procedure and a functional form...
Y. Okabe , M. Kikuchi and K. Ohno
Prog. Theor. Phys.   75 496-505   Apr 1986   [Refereed]
M. Kikuchi and Y. Okabe
Prog. Theor. Phys.   75(1) 192-194   Apr 1986   [Refereed]
M. Kikuchi and Y. Okabe
Prog. Theor. Phys.   74 458-467   Apr 1985   [Refereed]
M. Kikuchi and Y. Okabe
Phys. Rev. Lett.   55 1220-1222   Apr 1985   [Refereed]
We report the first Monte Carlo simulation on the critical relaxation of the three-dimensional kinetic Ising model with free surfaces. The surface-layer magnetization is shown to relax as t^{?β1/νz} at T=Tc, while the bulk magnetization relaxes as...
M. Kikuchi and Y. Okabe
Prog. Theor. Phys.   73 32-40   Apr 1985   [Refereed]
Monte Carlo technique is applied to the three-dimensional Ising model with free surface. The critical behavior of the layer magnetization, the layer susceptibility and the local susceptibility near the ordinary transition point is investigated. Th...